[Chimera-users] Autodock Vina plugin

[Enrico Martinez]

Thank you very much, Eric!
I actually tried to remove all hydrogens from the protein and ligand
and in that case there was an error related to prepare_ligand4.py

then I removed hydrogens only from the protein (keeping them for the
ligand) and got new error:
Service 'local:' is unavailable.  See Reply Log for more details.
Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto
adding gasteiger charges to peptide
'Deleting non-standard residues: from test.receptor
Wrote test.ligand.pdb into /Users/gleb/Desktop/docking_tuto
Traceback from web application request:
Traceback (most recent call last):
  File "/Applications/Chimera.app/Contents/Resources/share/WebServices/appWebService.py",
line 48, in _initApp
    self.backend = Backend(service, url)
  File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_local.py",
line 59, in __init__
    % self.exePath)
UserError: "" is not an executable
Service 'local:' is unavailable.  See Reply Log for more details.

вт, 4 янв. 2022 г. в 19:20, Eric Pettersen <pett at cgl.ucsf.edu>:
>
> Hi,
>         Autodock Vina is getting tripped up by hydrogen names it doesn't expect. Try this: delete all hydrogens with the command (Favorites→Command Line) "del H". Then under "Receptor options" in the AutoDock Vina panel change "Add hydrogens in Chimera" to "false".
>
> --Eric
>
>         Eric Pettersen
>         UCSF Computer Graphics Lab
>
>
> > On Jan 4, 2022, at 7:27 AM, Enrico Martinez via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera Users,
> > First Happy New Year to you and your families!
> >
> > I am trying to perform protein-ligand docking using UCSF Chimera 1.16v
> > installed on my iMAC Big Sur.
> > Using the pdb of the receptor and mol2 of the ligand (that I have
> > already tested with VINA 1.2.3!) I got the following error:
> > Model 1 (receptor.pdb) appears to be a protein without secondary
> > structure assignments.
> > Automatically computing assignments using 'ksdssp' and parameter values:
> >  energy cutoff -0.5
> >  minimum helix length 3
> >  minimum strand length 3
> > Use command 'help ksdssp' for more information.
> > No SEQRES records for receptor.pdb (#1) chain A; guessing terminii instead
> > Chain-initial residues that are actual N terminii: #1 SER 1.A
> > Chain-initial residues that are not actual N terminii:
> > Chain-final residues that are actual C terminii:
> > Chain-final residues that are not actual C terminii: #1 THR 304.A
> > 278 hydrogen bonds
> > Removing spurious proton from 'C' of #1 THR 304.A
> > Hydrogens added
> > Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto
> > adding gasteiger charges to peptide
> > Traceback (most recent call last):
> >  File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py",
> > line 395, in prepareReceptor
> >    execfile(scriptPath, d)
> >  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py",
> > line 172, in <module>
> >    delete_single_nonstd_residues=delete_single_nonstd_residues)
> >  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py",
> > line 533, in __init__
> >    version=version,
> > delete_single_nonstd_residues=delete_single_nonstd_residues)
> >  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py",
> > line 140, in __init__
> >    self.addCharges(mol, charges_to_add)
> >  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py",
> > line 226, in addCharges
> >    chargeCalculator.addCharges(mol.allAtoms)
> >  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py",
> > line 80, in addCharges
> >    babel.assignHybridization(atoms)
> >  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py",
> > line 127, in assignHybridization
> >    a.babel_atomic_number = self.get_atomic_number(a.babel_type)
> >  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py",
> > line 103, in get_atomic_number
> >    (name,_name) )
> > ValueError: Could not find atomic number for Hn Hn
> > Receptor preparation for AutoDock Vina failed; please look in Reply
> > Log to see error messages.cannot prepare receptor for AutoDock Vina;
> > please look in Reply Log and/or run Chimera with --debug flag to see
> > errors.
> >
> > So here are my questions:
> > 1) May this error be related to the version of OSX installed on my
> > imac (I can not run MGL tools on the Big Sur for instance) ??
> >
> > 2) Alternatively may I use the ADT scripts integrated in the Chimera
> > like prepare_receptor4.py for my scripting purposes (outside of the
> > UCSF Chimera) on the same iMAC machine ?
> >
> > Many thanks in advance!
> > Cheers
> > Enrico
> > _______________________________________________
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> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>